The second day in our "recovery" phase: A system isn't exactly "safe" after the malware is removed. What you actually need to figure out is how the system got compromissed in the first place, and how to prevent a future compromisse. As already pointed out, just removing the malware will just get you back to getting exploited again.

What software and what tricks do you use to:

make sure the vulnerability was remidiated?

acertain some level of confidence that the malware didn't leave behind any backdoors?

Nessus, a popular vulnerability scanner, has recently changed licenses. Did this affect you (or not)? Are there any alternatives?

How do you continually monitor systems as new vulnerabilities and patches are released all the time.